Skip to contents

Contributing to Shennong

Source: CONTRIBUTING.md

Development workflow

Use small, reviewable changes. Prefer one focused behavior change per commit, with matching tests and documentation updates.

Before opening a pull request, run:

devtools::document()
testthat::test_local(stop_on_failure = TRUE)

And from the shell:

R CMD build .
R CMD check --no-manual Shennong_*.tar.gz

Documentation

  • Edit roxygen comments in R/ and regenerate man/ with devtools::document().
  • Edit README.Rmd, then rebuild README.md.
  • Keep vignette chunks safe for package checks. Heavy or networked workflows must be guarded.

Testing

  • Add tests for the public behavior you touch.
  • Prefer lightweight fixtures and synthetic matrices over network downloads.
  • Skip optional-package tests with skip_if_not_installed() when appropriate.

Commit messages

This repository uses Conventional Commits.

Preferred format:

<type>(<scope>): <summary>

Examples:

  • feat(clustering): consolidate single and harmony workflows
  • fix(io): preserve row names in metadata import
  • docs(readme): expand quick-start examples
  • test(preprocessing): cover qc filtering helpers

Recommended types:

  • feat
  • fix
  • refactor
  • docs
  • test
  • build
  • ci
  • chore

Breaking changes should use ! and be documented in NEWS.md.